rs4097766

chr1-157250762-G-Achr1-157250762-G-T

Variant summary

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

The XR_922183.3(LOC105371456):n.510+1644C>T 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 0.0353 in 152,116 control chromosomes in the GnomAD database, including 193 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 0.035 (193 hom., cov: 32)
• Consequence: LOC105371456 XR_922183.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

Genes affected

LOC105371456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371456	XR_922183.3	n.510+1644C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0352 AC: 5356 AN: 152000 Hom.: 191 Cov.: 32

Gnomad AFR AF: 0.0402

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0987

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.0810

Gnomad SAS AF: 0.0502

Gnomad FIN AF: 0.0108

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0183

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0353 AC: 5370 AN: 152116 Hom.: 193 Cov.: 32 AF XY: 0.0363 AC XY: 2703 AN XY: 74374

Gnomad4 AFR AF: 0.0403

Gnomad4 AMR AF: 0.0990

Gnomad4 ASJ AF: 0.00259

Gnomad4 EAS AF: 0.0810

Gnomad4 SAS AF: 0.0499

Gnomad4 FIN AF: 0.0108

Gnomad4 NFE AF: 0.0183

Gnomad4 OTH AF: 0.0299

Alfa AF: 0.0105 Hom.: 0

Bravo AF: 0.0429

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.3
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4097766; hg19: chr1-157220552;