rs11761324

Variant names:

• chr7-77803597-A-G
• rs11761324
• NM_001395272.1:c.-36+4626A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-77803597-A-G
• chr7-77803597-A-T

Variant summary

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

The NM_001395272.1(PHTF2):​c.-36+4626A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,000 control chromosomes in the GnomAD database, including 4,119 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 0.22 (4119 hom., cov: 32)
• Consequence: PHTF2 NM_001395272.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427
• Publications: 7 publications found

Genes affected

PHTF2 (HGNC:13411): (putative homeodomain transcription factor 2) Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395272.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHTF2	NM_001395272.1	MANE Select	c.-36+4626A>G		intron	N/A	NP_001382201.1	Q8N3S3-2
	PHTF2	NM_001127358.2		c.-36+4626A>G		intron	N/A	NP_001120830.1	Q8N3S3-3
	PHTF2	NM_001366086.1		c.-36+4514A>G		intron	N/A	NP_001353015.1	Q8N3S3-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHTF2	ENST00000422959.8	TSL:5 MANE Select	c.-36+4626A>G		intron	N/A	ENSP00000403042.2	Q8N3S3-2
	PHTF2	ENST00000307305.12	TSL:1	c.-36+4626A>G		intron	N/A	ENSP00000307699.8	Q8N3S3-3
	PHTF2	ENST00000275575.11	TSL:1	c.-36+4626A>G		intron	N/A	ENSP00000275575.7	Q8N3S3-4

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34078 AN: 151882 Hom.: 4113 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.224 AC: 34098 AN: 152000 Hom.: 4119 Cov.: 32 AF XY: 0.223 AC XY: 16539 AN XY: 74292

African (AFR) AF: 0.153 AC: 6342 AN: 41478

American (AMR) AF: 0.234 AC: 3575 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 895 AN: 3468

East Asian (EAS) AF: 0.143 AC: 739 AN: 5176

South Asian (SAS) AF: 0.292 AC: 1408 AN: 4826

European-Finnish (FIN) AF: 0.233 AC: 2456 AN: 10534

Middle Eastern (MID) AF: 0.252 AC: 73 AN: 290

European-Non Finnish (NFE) AF: 0.264 AC: 17960 AN: 67934

Other (OTH) AF: 0.237 AC: 500 AN: 2114

Alfa AF: 0.255 Hom.: 7704

Bravo AF: 0.218

Asia WGS AF: 0.221 AC: 770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	12
DANN	Benign	0.51
PhyloP100		0.43
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: rs11761324; hg19: chr7-77432914;