rs7649861

Positions:

• chr3-144451858-G-A
• chr3-144451858-G-C

Variant summary

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

The XR_007096124.1(LOC105374140):​n.20164-16228G>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 0.634 in 152,008 control chromosomes in the GnomAD database, including 31,297 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 0.63 (31297 hom., cov: 32)
• Consequence: LOC105374140 XR_007096124.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

Genes affected

LOC105374140 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374140	XR_007096124.1	n.20164-16228G>A		intron_variant, non_coding_transcript_variant
LOC105374140	XR_001740941.2	n.20091-16228G>A		intron_variant, non_coding_transcript_variant
LOC105374140	XR_001740943.3	n.163-16228G>A		intron_variant, non_coding_transcript_variant
LOC105374140	XR_924558.4	n.254-16228G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96357 AN: 151890 Hom.: 31272 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.670

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.634 AC: 96430 AN: 152008 Hom.: 31297 Cov.: 32 AF XY: 0.630 AC XY: 46820 AN XY: 74286

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.640

Alfa AF: 0.626 Hom.: 13659

Bravo AF: 0.636

Asia WGS AF: 0.570 AC: 1983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.31
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7649861; hg19: chr3-144170700;