rs3935401

Variant names:

• chr1-161363768-A-G
• rs3935401

Your query was ambiguous. Multiple possible variants found:

• chr1-161363768-A-G
• chr1-161363768-A-C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.112 in 232,898 control chromosomes in the GnomAD database, including 2,186 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.12 (1420 hom., cov: 32)
  • Exomes 𝑓: 0.10 (766 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0340
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BP6: Variant 1-161363768-A-G is Benign according to our data. Variant chr1-161363768-A-G is described in ClinVar as Benign. ClinVar VariationId is 293347.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17801 AN: 152064 Hom.: 1417 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0687

Gnomad ASJ AF: 0.0282

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0643

Gnomad OTH AF: 0.0930

GnomAD4 exome AF: 0.101 AC: 8183 AN: 80718 Hom.: 766 Cov.: 0 AF XY: 0.0976 AC XY: 3622 AN XY: 37124

African (AFR) AF: 0.223 AC: 869 AN: 3890

American (AMR) AF: 0.0635 AC: 158 AN: 2490

Ashkenazi Jewish (ASJ) AF: 0.0310 AC: 158 AN: 5100

East Asian (EAS) AF: 0.303 AC: 3488 AN: 11504

South Asian (SAS) AF: 0.209 AC: 146 AN: 698

European-Finnish (FIN) AF: 0.0517 AC: 3 AN: 58

Middle Eastern (MID) AF: 0.0391 AC: 19 AN: 486

European-Non Finnish (NFE) AF: 0.0568 AC: 2825 AN: 49754

Other (OTH) AF: 0.0767 AC: 517 AN: 6738

GnomAD4 genome AF: 0.117 AC: 17823 AN: 152180 Hom.: 1420 Cov.: 32 AF XY: 0.120 AC XY: 8914 AN XY: 74418

African (AFR) AF: 0.216 AC: 8979 AN: 41512

American (AMR) AF: 0.0685 AC: 1048 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0282 AC: 98 AN: 3472

East Asian (EAS) AF: 0.210 AC: 1084 AN: 5168

South Asian (SAS) AF: 0.186 AC: 895 AN: 4820

European-Finnish (FIN) AF: 0.104 AC: 1106 AN: 10596

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0643 AC: 4370 AN: 68002

Other (OTH) AF: 0.0920 AC: 194 AN: 2108

Alfa AF: 0.0716 Hom.: 703

Bravo AF: 0.115

Asia WGS AF: 0.202 AC: 698 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Hereditary pheochromocytoma-paraganglioma (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.41
PhyloP100		-0.034
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Other links and lift over

dbSNP: rs3935401; hg19: chr1-161333558;