rs4602918

Positions:

• chr8-2765531-T-C
• chr8-2765531-T-G

Variant summary

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

The NR_168443.1(LOC105377785):​n.538+38038T>C 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 0.452 in 151,994 control chromosomes in the GnomAD database, including 20,560 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 0.45 (20560 hom., cov: 33)
• Consequence: LOC105377785 NR_168443.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377785	NR_168443.1	n.538+38038T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654515.1	n.531+38038T>C		intron_variant, non_coding_transcript_variant
	ENST00000520024.1	n.176+38038T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000670600.1	n.538+38038T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68551 AN: 151876 Hom.: 20504 Cov.: 33

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.452 AC: 68665 AN: 151994 Hom.: 20560 Cov.: 33 AF XY: 0.454 AC XY: 33706 AN XY: 74320

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.417

Alfa AF: 0.358 Hom.: 1691

Bravo AF: 0.492

Asia WGS AF: 0.437 AC: 1517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.63
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4602918; hg19: chr8-2623069;