rs71838136

Variant names:

• chr7-156681085-TA-T
• rs71838136
• NM_022458.4:c.*2992delT

Your query was ambiguous. Multiple possible variants found:

• chr7-156681085-TA-T
• chr7-156681085-TA-TAA
• chr7-156681085-TA-TAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_022458.4(LMBR1):​c.*2992delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00585 in 373,742 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0016 (2 hom., cov: 21)
  • Exomes 𝑓: 0.0087 (1 hom.)
• Consequence: LMBR1 NM_022458.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774

Genes affected

LMBR1 (HGNC:13243): (limb development membrane protein 1) This gene encodes a member of the LMBR1-like membrane protein family. Another member of this protein family has been shown to be a lipocalin transmembrane receptor. A highly conserved, cis-acting regulatory module for the sonic hedgehog gene is located within an intron of this gene. Consequently, disruption of this genic region can alter sonic hedgehog expression and affect limb patterning, but it is not known if this gene functions directly in limb development. Mutations and chromosomal deletions and rearrangements in this genic region are associated with acheiropody and preaxial polydactyly, which likely result from altered sonic hedgehog expression. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00157 (233/148808) while in subpopulation AFR AF= 0.00541 (219/40456). AF 95% confidence interval is 0.00483. There are 2 homozygotes in gnomad4. There are 111 alleles in male gnomad4 subpopulation. Median coverage is 21. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 2 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMBR1	NM_022458.4	c.*2992delT		3_prime_UTR_variant	Exon 17 of 17	ENST00000353442.10	NP_071903.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LMBR1	ENST00000353442	c.*2992delT		3_prime_UTR_variant	Exon 17 of 17	1	NM_022458.4	ENSP00000326604.7
LMBR1	ENST00000430825.3	n.266-512delT		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.00154 AC: 229 AN: 148718 Hom.: 2 Cov.: 21

Gnomad AFR AF: 0.00533

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000134

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000516

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000893

Gnomad OTH AF: 0.000488

GnomAD4 exome AF: 0.00869 AC: 1955 AN: 224934 Hom.: 1 Cov.: 0 AF XY: 0.00786 AC XY: 1027 AN XY: 130624

Gnomad4 AFR exome AF: 0.0350

Gnomad4 AMR exome AF: 0.0206

Gnomad4 ASJ exome AF: 0.00554

Gnomad4 EAS exome AF: 0.0342

Gnomad4 SAS exome AF: 0.00709

Gnomad4 FIN exome AF: 0.00556

Gnomad4 NFE exome AF: 0.00627

Gnomad4 OTH exome AF: 0.00906

GnomAD4 genome AF: 0.00157 AC: 233 AN: 148808 Hom.: 2 Cov.: 21 AF XY: 0.00153 AC XY: 111 AN XY: 72572

Gnomad4 AFR AF: 0.00541

Gnomad4 AMR AF: 0.000134

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000516

Gnomad4 NFE AF: 0.0000894

Gnomad4 OTH AF: 0.000483

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs71838136; hg19: chr7-156473779;