2-61824389-G-A

Position:

• chr2-61824389-G-A

Variant summary

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

The XM_047445962.1(FAM161A):​c.1838+2715C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,622 control chromosomes in the GnomAD database, including 10,757 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 0.36 (10757 hom., cov: 30)
• Consequence: FAM161A XM_047445962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311

Genes affected

FAM161A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM161A	XM_047445962.1	c.1838+2715C>T		intron_variant
FAM161A	XR_001738972.3	n.2025+2715C>T		intron_variant, non_coding_transcript_variant
FAM161A	XR_007082540.1	n.2025+2715C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55184 AN: 151506 Hom.: 10735 Cov.: 30

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.364 AC: 55237 AN: 151622 Hom.: 10757 Cov.: 30 AF XY: 0.376 AC XY: 27809 AN XY: 74054

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.372

Alfa AF: 0.344 Hom.: 15783

Bravo AF: 0.365

Asia WGS AF: 0.584 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1919481; hg19: chr2-62051524;