4-180511711-C-T

Position:

• chr4-180511711-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_939517.3(LOC105377565):​n.185+16425G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,948 control chromosomes in the GnomAD database, including 26,378 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (26378 hom., cov: 32)
• Consequence: LOC105377565 XR_939517.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.880

Genes affected

LOC105377567 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377567	XR_007058395.1	n.1311-27960C>T		intron_variant, non_coding_transcript_variant
LOC105377565	XR_939517.3	n.185+16425G>A		intron_variant, non_coding_transcript_variant
LOC105377567	XR_001741469.2	n.1400-27960C>T		intron_variant, non_coding_transcript_variant
LOC105377567	XR_007058394.1	n.2210-27960C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88854 AN: 151830 Hom.: 26353 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.578

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.585 AC: 88921 AN: 151948 Hom.: 26378 Cov.: 32 AF XY: 0.589 AC XY: 43752 AN XY: 74284

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.581

Alfa AF: 0.598 Hom.: 3296

Bravo AF: 0.579

Asia WGS AF: 0.591 AC: 2053 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.34
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2546613; hg19: chr4-181432864;