1-15359301-T-C

Variant names:

• chr1-15359301-T-C
• rs488595
• NM_001391957.1:c.2736+1018T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001391957.1(FHAD1):​c.2736+1018T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 151,870 control chromosomes in the GnomAD database, including 31,063 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 0.62 (31063 hom., cov: 30)
• Consequence: FHAD1 NM_001391957.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569
• Publications: 4 publications found

Genes affected

FHAD1 (HGNC:29408): (forkhead associated phosphopeptide binding domain 1)

EFHD2-AS1 (HGNC:55801): (EFHD2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FHAD1	NM_001391957.1	c.2736+1018T>C		intron_variant	Intron 21 of 33	ENST00000688493.1	NP_001378886.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FHAD1	ENST00000688493.1	c.2736+1018T>C		intron_variant	Intron 21 of 33		NM_001391957.1	ENSP00000509124.1

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94762 AN: 151750 Hom.: 31016 Cov.: 30

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.625 AC: 94866 AN: 151870 Hom.: 31063 Cov.: 30 AF XY: 0.623 AC XY: 46220 AN XY: 74216

African (AFR) AF: 0.832 AC: 34504 AN: 41496

American (AMR) AF: 0.580 AC: 8857 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1988 AN: 3470

East Asian (EAS) AF: 0.771 AC: 3963 AN: 5142

South Asian (SAS) AF: 0.539 AC: 2581 AN: 4790

European-Finnish (FIN) AF: 0.526 AC: 5527 AN: 10514

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35452 AN: 67880

Other (OTH) AF: 0.620 AC: 1307 AN: 2108

Alfa AF: 0.574 Hom.: 9862

Bravo AF: 0.639

Asia WGS AF: 0.671 AC: 2334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.76
PhyloP100		-0.57
Mutation Taster		=100/0	polymorphism (auto)

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: rs488595; hg19: chr1-15685797;